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The BioGRID interaction database: 2019 update

Rose Oughtred, Chris Stark, Bobby-Joe Breitkreutz, Jennifer Rust, Lorrie Boucher, Christie Chang, Nadine Kolas, Lara O'Donnell, Genie Leung, Rochelle McAdam, Frederick Zhang, Sonam Dolma (+5 others)
2018 Nucleic Acids Research  
The Biological General Repository for Interaction Datasets (BioGRID: is an open access database dedicated to the curation and archival storage of protein, genetic and chemical interactions  ...  BioGRID now captures chemical interaction data, including chemical-protein interactions for human drug targets drawn from the DrugBank database and manually curated bioactive compounds reported in the  ...  ACKNOWLEDGEMENTS The authors thank John Aitchison, Brenda Andrews, Gary Bader, Anastasia Baryshnikova  ... 
doi:10.1093/nar/gky1079 pmid:30476227 pmcid:PMC6324058 fatcat:72ppbdg3vbbhzfeugxmqu7athm

The BioGRID interaction database: 2013 update

Andrew Chatr-aryamontri, Bobby-Joe Breitkreutz, Sven Heinicke, Lorrie Boucher, Andrew Winter, Chris Stark, Julie Nixon, Lindsay Ramage, Nadine Kolas, Lara O'Donnell, Teresa Reguly, Ashton Breitkreutz (+8 others)
2012 Nucleic Acids Research  
This dataset represents interaction records for 66 model organisms and represents a 30% increase compared to the previous 2015 BioGRID update.  ...  The Biological General Repository for Interaction Datasets (BioGRID: is an open access database dedicated to the annotation and archival of protein, genetic and chemical interactions  ...  ACKNOWLEDGEMENTS The authors thank Chris Grove, Paul Sternberg and Anastasia Baryshnikova for ongoing collaborative development of the Genetic Interaction Structured Terminology.  ... 
doi:10.1093/nar/gks1158 pmid:23203989 pmcid:PMC3531226 fatcat:nmn2ijk3qje6jfpsgpzgk2p2nm

The Comparative Toxicogenomics Database: update 2017

Allan Peter Davis, Cynthia J. Grondin, Robin J. Johnson, Daniela Sciaky, Benjamin L. King, Roy McMorran, Jolene Wiegers, Thomas C. Wiegers, Carolyn J. Mattingly
2016 Nucleic Acids Research  
The Comparative Toxicogenomics Database (CTD; provides information about interactions between chemicals and gene products, and their relationships to diseases.  ...  Core CTD content (chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature) are integrated with each other as well as with select external datasets to generate  ...  (A) CTD's new 'Exposure Studies' query page (http:// D976 Nucleic Acids Research, 2017, Vol. 45, Database issue Figure 3 3 Figure 3.  ... 
doi:10.1093/nar/gkw838 pmid:27651457 pmcid:PMC5210612 fatcat:povogyqyofcebnljc3jnl4fnoq

MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes

Ludwig C. Hinske, Felipe R. C. dos Santos, Daniel T. Ohara, Lucila Ohno-Machado, Simone Kreth, Pedro A. F. Galante
2017 Database: The Journal of Biological Databases and Curation  
MiRIAD is a database with an interactive and user-friendly online interface that has been facilitating research on intragenic miRNAs. In this article, we present a major update.  ...  Although the previous version solely reported protein interactions, the update features a separate network analysis view that can either be accessed V C The Author(s) through the submission of a list of  ...  Acknowledgements The authors thank Gustavo S. Franc¸a for working on the previous miRIAD version as well as Anamaria A. Camargo and Luiz F. L. Reis for their valuable suggestions.  ... 
doi:10.1093/database/bax053 pmid:29220447 pmcid:PMC5569676 fatcat:j6h6gfuwgbezfa2r2mlyjsucca

KiPho: malaria parasite kinome and phosphatome portal

Rajan Pandey, Pawan Kumar, Dinesh Gupta
2017 Database: The Journal of Biological Databases and Curation  
Additionally, we have incorporated relevant and manually curated data, which will be updated from time to time with the availability of new information.  ...  The Plasmodium kinases and phosphatases play an essential role in the regulation of substrate reversible-phosphorylation and overall cellular homeostasis.  ...  Database, Vol. 2017, Article ID bax063  ... 
doi:10.1093/database/bax063 pmid:29220464 pmcid:PMC5737071 fatcat:svl76ahoivd5vescvimp6nzkme

Measuring pathway database coverage of the phosphoproteome

Hannah Huckstep, Liam G. Fearnley, Melissa J. Davis
2021 PeerJ  
We first determined the global coverage of each database at both the protein and phosphosite level.  ...  Finally, we looked in detail at the coverage of each database over six experimental datasets.  ...  ACKNOWLEDGEMENTS The authors thank Daniel Esposito, Samuel Lee and Dharmesh Bhuva for technical support. ADDITIONAL INFORMATION AND DECLARATIONS  ... 
doi:10.7717/peerj.11298 pmid:34113485 pmcid:PMC8162239 fatcat:yx4zibz3cvcm7h344ie3g2ge5u

Protein-Protein Interaction Interface Database Development based on Protein Network

Mr. Kamlesh K. Gautam
2017 IJARCCE  
Protein-Protein interaction interface database (PPIIDB) is developing on the basis of cellular and biological processes of protein-protein interaction interfaces of protein network.  ...  energy (∆G), Cluster Coefficient (CC), Connectivity, Degree of node or Degree of network, Euclidean Distance between interacted proteins, Network Interaction Modularity (Im), size of interface or Voronoi  ...  ANALYSES OF VARIOUS DATABASES We have analysis various Databases, like the PINT, Protorp, HPRD, BioGRID, BIND, IntAct, MIPS, APID, DIP, and MINT these all databases provide the lists of experimental and  ... 
doi:10.17148/ijarcce.2017.63211 fatcat:lotwvtx6jna4zofxz4drm7ohfi

PICKLE 3.0: Enriching the human Meta-database with the mouse protein interactome extended via mouse-human orthology

Georgios N Dimitrakopoulos, Maria I Klapa, Nicholas K Moschonas, Pier Luigi Martelli
2020 Bioinformatics  
Summary The PICKLE 3.0 upgrade refers to the enrichment of this human protein-protein interaction (PPI) meta-database with the mouse protein interactome.  ...  The relational scheme of PICKLE 3.0 has been amended to exploit the Mouse Genome Informatics (MGI) mouse-human ortholog gene pair collection, enabling (i) the extension through orthology of the mouse interactome  ...  Introduction Protein InteraCtion KnowLegdE (PICKLE) meta-database has been developed to consistently integrate primary human PPI datasets (Gioutlakis et al, 2017; Klapa et al, 2013) .  ... 
doi:10.1093/bioinformatics/btaa1070 pmid:33367505 pmcid:PMC8034533 fatcat:q4tmssyesnaujcabqpvtcpclqq

YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules

Wei-Sheng Wu, Pin-Han Chen, Tsung-Te Chen, Yan-Yuan Tseng
2017 Database: The Journal of Biological Databases and Curation  
in the GM.  ...  Since Cbf1-Met4-Met32 is known to regulate genes in sulfur amino acid biosynthesis pathway, we test the overlap between the set of genes in the sulfur amino acid biosynthesis pathway and the set of genes  ...  In the future, we plan to improve YGMD as follows. First, we will keep updating our database once updated data in SGD, YEASTRACT, BioGRID, CoopTFD and YeastNet are available.  ... 
doi:10.1093/database/bax085 pmid:29220473 pmcid:PMC5691354 fatcat:qhrubmmjy5fijb7o7af76u6pdq

How helpful are the protein-protein interaction databases and which ones? [article]

Akhilesh Kumar Bajpai, Sravanthi Davuluri, Kriti Tiwary, Sithalechumi Narayanan, Sailaja Oguru, Kavyashree Basavaraju, Deena Dayalan, Kavitha Thirumurugan, Kshitish K Acharya
2019 bioRxiv   pre-print
Protein-protein interactions (PPIs) are critical, and so are the databases and tools (resources) concerning PPIs.  ...  Overall, hPRINT, STRING and IID together retrieved ~94% of 'total' protein interactions available in the databases. The coverage of certain databases was skewed for some gene-types.  ...  Acknowledgements The authors thank colleagues at BdataA and Shodhaka Life Sciences Pvt. Ltd. for assistance in gathering some of the PPI data and analysis.  ... 
doi:10.1101/566372 fatcat:f46uga34djaarbpao2wgvzldu4

PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology

Aris Gioutlakis, Maria I. Klapa, Nicholas K. Moschonas, Baldo Oliva
2017 PLoS ONE  
used for identification of normalization biases, and enables the appraisal of potential false positive interactions through PPI source database cross-checking.  ...  PICKLE (Protein InteraCtion KnowLedgebasE) 2.0 implements a new architecture for this recently introduced human PPI meta-database.  ...  .0186039 October 12, 2017 17 / 17  ... 
doi:10.1371/journal.pone.0186039 pmid:29023571 pmcid:PMC5638325 fatcat:nvhuozyp2je33gw7m23epeler4

Predicted rat interactome database and gene set linkage analysis

Yu-Tian Tao, Xiao-Bao Ding, Jie Jin, Hai-Bo Zhang, Wen-Ping Guo, Li Ruan, Qiao-Lei Yang, Peng-Cheng Chen, Heng Yao, Xin Chen
2020 Database: The Journal of Biological Databases and Curation  
To facilitate molecular pharmacology studies in rats, we present the predicted rat interactome database (PRID), which is a database of high-quality predicted functional gene interactions with balanced  ...  PRID integrates functional gene association data from 10 public databases and infers 305 939 putative functional associations, which are expected to include 13.02% of all rat protein interactions, and  ...  Some of these databases integrate the experimentally reported protein-protein interactions, such as RGD (14) , BioGrid (15) and IntAct (16) .  ... 
doi:10.1093/database/baaa086 pmid:33216897 pmcid:PMC7678787 fatcat:g4fsyhzbt5g7xniqgvvdz2r2ai

mPPI: a database extension to visualize structural interactome in a one-to-many manner

Yekai Zhou, Hongjun Chen, Sida Li, Ming Chen
2021 Database: The Journal of Biological Databases and Curation  
Protein–protein interaction (PPI) databases with structural information are useful to investigate biological functions at both systematic and atomic levels.  ...  From the perspective of the display and function of PPI, as well as the structural binding interface, the related database and resources are summarized.  ...  The duplication was because most indexed entries were from literature mining, which has not excluded the submission of database updates.  ... 
doi:10.1093/database/baab036 pmid:34156447 fatcat:jehgi5sty5birgsr6dez3iwr4u

mutTCPdb: a comprehensive database for genomic variants of a tropical country neglected disease—tropical calcific pancreatitis

Garima Singh, Basharat Bhat, M S K Jayadev, Ch Madhusudhan, Ashutosh Singh
2018 Database: The Journal of Biological Databases and Curation  
Several existing databases such as the dbSNP, Uniprot, miRTarBase2.0, HGNC, PFAM, KEGG, PROSITE, MINT, BIOGRID 3.4 and Ensemble Genome Browser 87 were queried to collect information specific to the gene  ...  The database is highly curated for diseasespecific gene variants and provides complete information on function, transcript information, pathways, interactions, miRNAs and PubMed references along with remarks  ...  Acknowledgement A.S. is thankful to Shiv Nadar University for providing all the necessary support to perform this study. Conflict of interest. None declared.  ... 
doi:10.1093/database/bay043 pmid:30053238 pmcid:PMC6059086 fatcat:sactgq45obefxkbiaysbl7ib6u

The Comparative Toxicogenomics Database: update 2019

2018 Nucleic Acids Research  
The Comparative Toxicogenomics Database (CTD; is a premier public resource for literature-based, manually curated associations between chemicals, gene products, phenotypes, diseases  ...  These updates continue to improve CTD and help inform new testable hypotheses about the etiology and mechanisms underlying environmentally influenced diseases.  ...  Here, we provide our biennial database update and describe our newly released chemical-phenotype module, advanced query and display tools for exposure science data, an extensive update to the MEDIC disease  ... 
doi:10.1093/nar/gky868 pmid:30247620 pmcid:PMC6323936 fatcat:4qvewpc42jhsvic7phptfwy6im
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